Starting phenix.real_space_refine on Wed Jan 22 11:21:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxj_42766/01_2025/8uxj_42766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxj_42766/01_2025/8uxj_42766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uxj_42766/01_2025/8uxj_42766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxj_42766/01_2025/8uxj_42766.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxj_42766/01_2025/8uxj_42766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxj_42766/01_2025/8uxj_42766.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42768 2.51 5 N 12060 2.21 5 O 14724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 280 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 69696 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "B" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "D" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "E" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "F" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "G" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "H" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "J" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "K" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "L" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "M" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "N" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "O" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Q" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "R" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "S" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "T" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "U" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "V" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "W" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "X" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Y" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Z" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "a" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "b" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "c" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "d" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "e" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "f" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "h" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "i" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "j" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "g" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Time building chain proxies: 28.48, per 1000 atoms: 0.41 Number of scatterers: 69696 At special positions: 0 Unit cell: (140.112, 137.61, 330.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 14724 8.00 N 12060 7.00 C 42768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.65 Conformation dependent library (CDL) restraints added in 7.2 seconds 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18000 Finding SS restraints... Secondary structure from input PDB file: 284 helices and 34 sheets defined 76.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 61 through 101 removed outlier: 3.957A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 179 through 234 removed outlier: 3.901A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 262 removed outlier: 3.961A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.989A pdb=" N SER A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 36 Processing helix chain 'B' and resid 45 through 61 Processing helix chain 'B' and resid 61 through 101 removed outlier: 4.051A pdb=" N VAL B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 Processing helix chain 'B' and resid 179 through 234 removed outlier: 4.101A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 262 removed outlier: 3.519A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.165A pdb=" N LEU B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 270' Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 62 through 101 Processing helix chain 'C' and resid 106 through 130 Processing helix chain 'C' and resid 179 through 234 removed outlier: 4.090A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.556A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.547A pdb=" N SER C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 36 removed outlier: 4.224A pdb=" N MET D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 61 Processing helix chain 'D' and resid 61 through 101 removed outlier: 4.053A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 Processing helix chain 'D' and resid 179 through 234 removed outlier: 3.999A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 3.957A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 4.301A pdb=" N LEU D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 270' Processing helix chain 'E' and resid 9 through 36 Processing helix chain 'E' and resid 45 through 61 Processing helix chain 'E' and resid 61 through 100 removed outlier: 4.061A pdb=" N VAL E 65 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 Processing helix chain 'E' and resid 179 through 234 removed outlier: 3.772A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 262 removed outlier: 4.140A pdb=" N GLU E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 266 Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.959A pdb=" N LEU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 272' Processing helix chain 'F' and resid 9 through 36 Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 61 through 101 removed outlier: 4.014A pdb=" N VAL F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 99 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 Processing helix chain 'F' and resid 166 through 170 removed outlier: 3.658A pdb=" N GLY F 170 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 234 removed outlier: 4.063A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 262 removed outlier: 4.036A pdb=" N GLU F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 265 No H-bonds generated for 'chain 'F' and resid 263 through 265' Processing helix chain 'F' and resid 266 through 271 removed outlier: 4.308A pdb=" N SER F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 266 through 271' Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.508A pdb=" N MET G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 61 through 101 removed outlier: 4.128A pdb=" N VAL G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 Processing helix chain 'G' and resid 179 through 234 removed outlier: 3.946A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 3.836A pdb=" N GLU G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN G 263 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 272 removed outlier: 3.534A pdb=" N SER G 267 " --> pdb=" O SER G 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 36 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 61 through 101 removed outlier: 4.245A pdb=" N VAL H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 Processing helix chain 'H' and resid 165 through 170 removed outlier: 3.830A pdb=" N GLY H 170 " --> pdb=" O ALA H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 234 removed outlier: 4.040A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 262 removed outlier: 3.539A pdb=" N GLU H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN H 245 " --> pdb=" O SER H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 272 removed outlier: 4.036A pdb=" N SER H 267 " --> pdb=" O SER H 264 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 269 " --> pdb=" O SER H 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.500A pdb=" N MET I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 61 through 101 removed outlier: 4.238A pdb=" N VAL I 65 " --> pdb=" O SER I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 Processing helix chain 'I' and resid 165 through 170 removed outlier: 3.952A pdb=" N GLY I 170 " --> pdb=" O ALA I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 234 removed outlier: 3.909A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 262 removed outlier: 3.902A pdb=" N GLU I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN I 245 " --> pdb=" O SER I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 266 Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.924A pdb=" N LEU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE I 272 " --> pdb=" O ILE I 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 267 through 272' Processing helix chain 'J' and resid 9 through 36 Processing helix chain 'J' and resid 45 through 61 Processing helix chain 'J' and resid 61 through 101 removed outlier: 4.226A pdb=" N VAL J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 Processing helix chain 'J' and resid 166 through 170 removed outlier: 3.829A pdb=" N GLY J 170 " --> pdb=" O ALA J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 234 removed outlier: 3.936A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 4.159A pdb=" N GLU J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN J 245 " --> pdb=" O SER J 241 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 272 removed outlier: 3.943A pdb=" N SER J 267 " --> pdb=" O SER J 264 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE J 268 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU J 269 " --> pdb=" O SER J 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 36 Processing helix chain 'K' and resid 45 through 61 Processing helix chain 'K' and resid 61 through 102 removed outlier: 4.040A pdb=" N VAL K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 Processing helix chain 'K' and resid 179 through 234 removed outlier: 4.037A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.668A pdb=" N GLU K 240 " --> pdb=" O ASP K 236 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 272 removed outlier: 4.190A pdb=" N SER K 267 " --> pdb=" O SER K 264 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU K 269 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 36 Processing helix chain 'L' and resid 45 through 61 Processing helix chain 'L' and resid 62 through 102 removed outlier: 3.804A pdb=" N ASP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 179 through 234 removed outlier: 3.937A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.939A pdb=" N GLU L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN L 245 " --> pdb=" O SER L 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 271 removed outlier: 4.332A pdb=" N LEU L 269 " --> pdb=" O SER L 265 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER L 270 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 265 through 271' Processing helix chain 'M' and resid 9 through 36 Processing helix chain 'M' and resid 45 through 61 Processing helix chain 'M' and resid 61 through 101 removed outlier: 4.186A pdb=" N VAL M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 Processing helix chain 'M' and resid 166 through 170 removed outlier: 3.623A pdb=" N GLY M 170 " --> pdb=" O ALA M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 234 removed outlier: 3.895A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 263 removed outlier: 3.550A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN M 245 " --> pdb=" O SER M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 266 No H-bonds generated for 'chain 'M' and resid 264 through 266' Processing helix chain 'M' and resid 267 through 272 removed outlier: 3.886A pdb=" N LEU M 271 " --> pdb=" O SER M 267 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE M 272 " --> pdb=" O ILE M 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 267 through 272' Processing helix chain 'N' and resid 9 through 36 Processing helix chain 'N' and resid 45 through 61 Processing helix chain 'N' and resid 61 through 101 removed outlier: 4.057A pdb=" N VAL N 65 " --> pdb=" O SER N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 Processing helix chain 'N' and resid 166 through 170 removed outlier: 3.570A pdb=" N GLY N 170 " --> pdb=" O ALA N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 234 removed outlier: 4.003A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.569A pdb=" N GLU N 240 " --> pdb=" O ASP N 236 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN N 245 " --> pdb=" O SER N 241 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN N 263 " --> pdb=" O SER N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 272 removed outlier: 4.351A pdb=" N LEU N 269 " --> pdb=" O SER N 265 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU N 271 " --> pdb=" O SER N 267 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE N 272 " --> pdb=" O ILE N 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 265 through 272' Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 Processing helix chain 'O' and resid 61 through 101 removed outlier: 4.250A pdb=" N VAL O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 Processing helix chain 'O' and resid 165 through 170 removed outlier: 3.933A pdb=" N GLY O 170 " --> pdb=" O ALA O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 234 removed outlier: 4.077A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 263 removed outlier: 3.803A pdb=" N THR O 249 " --> pdb=" O GLN O 245 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN O 263 " --> pdb=" O SER O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 272 removed outlier: 3.856A pdb=" N SER O 267 " --> pdb=" O SER O 264 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER O 270 " --> pdb=" O SER O 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 36 Processing helix chain 'P' and resid 45 through 61 Processing helix chain 'P' and resid 61 through 102 removed outlier: 4.245A pdb=" N VAL P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP P 102 " --> pdb=" O LEU P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 Processing helix chain 'P' and resid 165 through 170 removed outlier: 3.946A pdb=" N GLY P 170 " --> pdb=" O ALA P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 234 removed outlier: 3.923A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 263 removed outlier: 3.536A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 272 removed outlier: 4.108A pdb=" N LEU P 269 " --> pdb=" O SER P 265 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER P 270 " --> pdb=" O SER P 266 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE P 272 " --> pdb=" O ILE P 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 265 through 272' Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.640A pdb=" N MET Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 61 Processing helix chain 'Q' and resid 61 through 101 removed outlier: 4.304A pdb=" N VAL Q 65 " --> pdb=" O SER Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 Processing helix chain 'Q' and resid 165 through 170 removed outlier: 3.813A pdb=" N GLY Q 170 " --> pdb=" O ALA Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 234 removed outlier: 3.979A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 263 removed outlier: 3.857A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN Q 263 " --> pdb=" O SER Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 272 removed outlier: 4.376A pdb=" N SER Q 267 " --> pdb=" O SER Q 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.653A pdb=" N MET R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 Processing helix chain 'R' and resid 61 through 101 removed outlier: 4.160A pdb=" N VAL R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 Processing helix chain 'R' and resid 166 through 170 removed outlier: 3.518A pdb=" N ILE R 169 " --> pdb=" O LEU R 166 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY R 170 " --> pdb=" O ALA R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 166 through 170' Processing helix chain 'R' and resid 179 through 234 removed outlier: 3.916A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 263 removed outlier: 3.876A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 271 removed outlier: 3.780A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 61 through 101 removed outlier: 4.317A pdb=" N VAL S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 Processing helix chain 'S' and resid 166 through 170 removed outlier: 3.879A pdb=" N GLY S 170 " --> pdb=" O ALA S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 234 removed outlier: 3.966A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 4.005A pdb=" N GLN S 263 " --> pdb=" O SER S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 266 No H-bonds generated for 'chain 'S' and resid 264 through 266' Processing helix chain 'S' and resid 267 through 272 removed outlier: 3.855A pdb=" N LEU S 271 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE S 272 " --> pdb=" O ILE S 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 267 through 272' Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.771A pdb=" N MET T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 61 Processing helix chain 'T' and resid 61 through 101 removed outlier: 4.229A pdb=" N VAL T 65 " --> pdb=" O SER T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 Processing helix chain 'T' and resid 165 through 170 removed outlier: 3.941A pdb=" N GLY T 170 " --> pdb=" O ALA T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 234 removed outlier: 3.914A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 264 Processing helix chain 'T' and resid 265 through 272 removed outlier: 3.805A pdb=" N ILE T 268 " --> pdb=" O SER T 265 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE T 272 " --> pdb=" O LEU T 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 36 removed outlier: 3.502A pdb=" N MET U 13 " --> pdb=" O ASN U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 61 Processing helix chain 'U' and resid 61 through 101 removed outlier: 4.081A pdb=" N VAL U 65 " --> pdb=" O SER U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 130 Processing helix chain 'U' and resid 166 through 170 removed outlier: 3.518A pdb=" N ILE U 169 " --> pdb=" O LEU U 166 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY U 170 " --> pdb=" O ALA U 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 166 through 170' Processing helix chain 'U' and resid 179 through 234 removed outlier: 4.016A pdb=" N GLY U 188 " --> pdb=" O LYS U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 236 through 263 removed outlier: 3.703A pdb=" N GLN U 263 " --> pdb=" O SER U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 266 No H-bonds generated for 'chain 'U' and resid 264 through 266' Processing helix chain 'U' and resid 267 through 272 removed outlier: 3.874A pdb=" N LEU U 271 " --> pdb=" O SER U 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE U 272 " --> pdb=" O ILE U 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 267 through 272' Processing helix chain 'V' and resid 9 through 36 removed outlier: 3.508A pdb=" N MET V 13 " --> pdb=" O ASN V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 61 Processing helix chain 'V' and resid 61 through 101 removed outlier: 4.045A pdb=" N VAL V 65 " --> pdb=" O SER V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 130 Processing helix chain 'V' and resid 165 through 170 removed outlier: 3.750A pdb=" N GLY V 170 " --> pdb=" O ALA V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 179 through 234 removed outlier: 3.961A pdb=" N GLY V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 236 through 264 Processing helix chain 'V' and resid 265 through 272 Processing helix chain 'W' and resid 9 through 36 removed outlier: 3.597A pdb=" N MET W 13 " --> pdb=" O ASN W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 61 Processing helix chain 'W' and resid 61 through 102 removed outlier: 4.149A pdb=" N VAL W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP W 102 " --> pdb=" O LEU W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 130 Processing helix chain 'W' and resid 166 through 170 removed outlier: 3.850A pdb=" N GLY W 170 " --> pdb=" O ALA W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 234 removed outlier: 3.950A pdb=" N GLY W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 263 removed outlier: 3.534A pdb=" N GLN W 245 " --> pdb=" O SER W 241 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN W 263 " --> pdb=" O SER W 259 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 272 removed outlier: 4.261A pdb=" N SER W 267 " --> pdb=" O SER W 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE W 268 " --> pdb=" O SER W 265 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE W 272 " --> pdb=" O LEU W 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 36 removed outlier: 3.567A pdb=" N MET X 13 " --> pdb=" O ASN X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 61 Processing helix chain 'X' and resid 62 through 102 removed outlier: 4.184A pdb=" N ASP X 102 " --> pdb=" O LEU X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 130 Processing helix chain 'X' and resid 179 through 234 removed outlier: 3.731A pdb=" N GLY X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 263 removed outlier: 3.649A pdb=" N GLN X 263 " --> pdb=" O SER X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.813A pdb=" N SER X 267 " --> pdb=" O SER X 264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 36 Processing helix chain 'Y' and resid 45 through 61 Processing helix chain 'Y' and resid 61 through 101 removed outlier: 4.231A pdb=" N VAL Y 65 " --> pdb=" O SER Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 130 Processing helix chain 'Y' and resid 179 through 234 removed outlier: 3.977A pdb=" N GLY Y 188 " --> pdb=" O LYS Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 263 removed outlier: 3.521A pdb=" N GLU Y 240 " --> pdb=" O ASP Y 236 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN Y 263 " --> pdb=" O SER Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 272 removed outlier: 4.125A pdb=" N SER Y 267 " --> pdb=" O SER Y 264 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 36 Processing helix chain 'Z' and resid 45 through 61 Processing helix chain 'Z' and resid 61 through 101 removed outlier: 4.242A pdb=" N VAL Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 131 removed outlier: 3.637A pdb=" N ALA Z 131 " --> pdb=" O ALA Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 170 removed outlier: 3.798A pdb=" N GLY Z 170 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 234 removed outlier: 4.052A pdb=" N GLY Z 188 " --> pdb=" O LYS Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 263 removed outlier: 3.561A pdb=" N GLU Z 240 " --> pdb=" O ASP Z 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 242 " --> pdb=" O ALA Z 238 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN Z 245 " --> pdb=" O SER Z 241 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN Z 263 " --> pdb=" O SER Z 259 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 272 removed outlier: 4.082A pdb=" N SER Z 267 " --> pdb=" O SER Z 264 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 36 removed outlier: 3.565A pdb=" N MET a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 61 Processing helix chain 'a' and resid 61 through 101 removed outlier: 4.267A pdb=" N VAL a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 106 through 130 Processing helix chain 'a' and resid 166 through 170 removed outlier: 3.691A pdb=" N GLY a 170 " --> pdb=" O ALA a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 234 removed outlier: 4.001A pdb=" N GLY a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 263 removed outlier: 3.588A pdb=" N GLU a 240 " --> pdb=" O ASP a 236 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN a 245 " --> pdb=" O SER a 241 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN a 263 " --> pdb=" O SER a 259 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 272 removed outlier: 4.178A pdb=" N SER a 270 " --> pdb=" O SER a 266 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU a 271 " --> pdb=" O SER a 267 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE a 272 " --> pdb=" O ILE a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 266 through 272' Processing helix chain 'b' and resid 9 through 36 Processing helix chain 'b' and resid 45 through 61 Processing helix chain 'b' and resid 61 through 101 removed outlier: 3.868A pdb=" N VAL b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 130 Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 179 through 234 removed outlier: 3.927A pdb=" N GLY b 188 " --> pdb=" O LYS b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 263 removed outlier: 3.705A pdb=" N GLU b 240 " --> pdb=" O ASP b 236 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN b 245 " --> pdb=" O SER b 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN b 263 " --> pdb=" O SER b 259 " (cutoff:3.500A) Processing helix chain 'b' and resid 265 through 270 removed outlier: 4.304A pdb=" N LEU b 269 " --> pdb=" O SER b 265 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER b 270 " --> pdb=" O SER b 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 265 through 270' Processing helix chain 'c' and resid 9 through 36 removed outlier: 3.548A pdb=" N MET c 13 " --> pdb=" O ASN c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 61 Processing helix chain 'c' and resid 61 through 102 removed outlier: 4.061A pdb=" N VAL c 65 " --> pdb=" O SER c 61 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP c 102 " --> pdb=" O LEU c 98 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 130 Processing helix chain 'c' and resid 179 through 234 removed outlier: 3.864A pdb=" N GLY c 188 " --> pdb=" O LYS c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 263 removed outlier: 3.614A pdb=" N GLN c 263 " --> pdb=" O SER c 259 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 272 removed outlier: 3.500A pdb=" N SER c 267 " --> pdb=" O SER c 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE c 268 " --> pdb=" O SER c 265 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 36 removed outlier: 3.574A pdb=" N MET d 13 " --> pdb=" O ASN d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 61 Processing helix chain 'd' and resid 61 through 102 removed outlier: 4.190A pdb=" N VAL d 65 " --> pdb=" O SER d 61 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP d 102 " --> pdb=" O LEU d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 130 Processing helix chain 'd' and resid 179 through 234 removed outlier: 3.763A pdb=" N GLY d 188 " --> pdb=" O LYS d 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU d 232 " --> pdb=" O GLY d 228 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL d 233 " --> pdb=" O VAL d 229 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 263 removed outlier: 3.718A pdb=" N GLU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN d 245 " --> pdb=" O SER d 241 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN d 263 " --> pdb=" O SER d 259 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 272 removed outlier: 3.723A pdb=" N SER d 267 " --> pdb=" O SER d 264 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 36 Processing helix chain 'e' and resid 45 through 61 Processing helix chain 'e' and resid 61 through 102 removed outlier: 4.044A pdb=" N VAL e 65 " --> pdb=" O SER e 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP e 102 " --> pdb=" O LEU e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 130 Processing helix chain 'e' and resid 165 through 170 Processing helix chain 'e' and resid 179 through 234 removed outlier: 4.354A pdb=" N GLY e 188 " --> pdb=" O LYS e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 263 removed outlier: 3.624A pdb=" N GLU e 240 " --> pdb=" O ASP e 236 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA e 242 " --> pdb=" O ALA e 238 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN e 263 " --> pdb=" O SER e 259 " (cutoff:3.500A) Processing helix chain 'e' and resid 264 through 272 removed outlier: 4.006A pdb=" N SER e 267 " --> pdb=" O SER e 264 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 36 Processing helix chain 'f' and resid 45 through 61 Processing helix chain 'f' and resid 61 through 101 removed outlier: 4.346A pdb=" N VAL f 65 " --> pdb=" O SER f 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 130 Processing helix chain 'f' and resid 166 through 170 removed outlier: 3.756A pdb=" N GLY f 170 " --> pdb=" O ALA f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 179 through 234 removed outlier: 3.813A pdb=" N GLY f 188 " --> pdb=" O LYS f 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 264 removed outlier: 3.826A pdb=" N GLU f 240 " --> pdb=" O ASP f 236 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN f 245 " --> pdb=" O SER f 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER f 264 " --> pdb=" O ILE f 260 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 272 removed outlier: 4.016A pdb=" N SER f 270 " --> pdb=" O SER f 266 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU f 271 " --> pdb=" O SER f 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE f 272 " --> pdb=" O ILE f 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 266 through 272' Processing helix chain 'h' and resid 9 through 36 Processing helix chain 'h' and resid 45 through 61 Processing helix chain 'h' and resid 61 through 102 removed outlier: 4.278A pdb=" N VAL h 65 " --> pdb=" O SER h 61 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP h 102 " --> pdb=" O LEU h 98 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 130 Processing helix chain 'h' and resid 166 through 170 Processing helix chain 'h' and resid 179 through 234 removed outlier: 3.994A pdb=" N GLY h 188 " --> pdb=" O LYS h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 263 removed outlier: 3.591A pdb=" N GLU h 240 " --> pdb=" O ASP h 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN h 245 " --> pdb=" O SER h 241 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN h 263 " --> pdb=" O SER h 259 " (cutoff:3.500A) Processing helix chain 'h' and resid 265 through 271 removed outlier: 4.219A pdb=" N LEU h 269 " --> pdb=" O SER h 265 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER h 270 " --> pdb=" O SER h 266 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU h 271 " --> pdb=" O SER h 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 265 through 271' Processing helix chain 'i' and resid 9 through 36 Processing helix chain 'i' and resid 45 through 61 Processing helix chain 'i' and resid 61 through 102 removed outlier: 3.915A pdb=" N VAL i 65 " --> pdb=" O SER i 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 130 Processing helix chain 'i' and resid 166 through 170 removed outlier: 3.520A pdb=" N ILE i 169 " --> pdb=" O LEU i 166 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY i 170 " --> pdb=" O ALA i 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 166 through 170' Processing helix chain 'i' and resid 179 through 234 removed outlier: 4.019A pdb=" N GLY i 188 " --> pdb=" O LYS i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 236 through 263 removed outlier: 3.653A pdb=" N GLU i 240 " --> pdb=" O ASP i 236 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA i 242 " --> pdb=" O ALA i 238 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN i 245 " --> pdb=" O SER i 241 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN i 263 " --> pdb=" O SER i 259 " (cutoff:3.500A) Processing helix chain 'i' and resid 265 through 270 removed outlier: 4.267A pdb=" N LEU i 269 " --> pdb=" O SER i 265 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER i 270 " --> pdb=" O SER i 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 265 through 270' Processing helix chain 'j' and resid 9 through 36 Processing helix chain 'j' and resid 45 through 61 Processing helix chain 'j' and resid 61 through 101 removed outlier: 3.977A pdb=" N VAL j 65 " --> pdb=" O SER j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 130 Processing helix chain 'j' and resid 166 through 170 removed outlier: 3.614A pdb=" N ILE j 169 " --> pdb=" O LEU j 166 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY j 170 " --> pdb=" O ALA j 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 166 through 170' Processing helix chain 'j' and resid 179 through 234 removed outlier: 3.958A pdb=" N GLY j 188 " --> pdb=" O LYS j 184 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 263 removed outlier: 3.557A pdb=" N GLU j 240 " --> pdb=" O ASP j 236 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA j 242 " --> pdb=" O ALA j 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN j 263 " --> pdb=" O SER j 259 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 266 No H-bonds generated for 'chain 'j' and resid 264 through 266' Processing helix chain 'j' and resid 267 through 272 removed outlier: 4.086A pdb=" N LEU j 271 " --> pdb=" O SER j 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE j 272 " --> pdb=" O ILE j 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 267 through 272' Processing helix chain 'g' and resid 9 through 36 removed outlier: 3.800A pdb=" N MET g 13 " --> pdb=" O ASN g 9 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY g 21 " --> pdb=" O GLN g 17 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 102 removed outlier: 4.442A pdb=" N ASN g 63 " --> pdb=" O ALA g 59 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL g 65 " --> pdb=" O SER g 61 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR g 85 " --> pdb=" O ALA g 81 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS g 94 " --> pdb=" O LEU g 90 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU g 95 " --> pdb=" O GLY g 91 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS g 96 " --> pdb=" O LYS g 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP g 102 " --> pdb=" O LEU g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 131 removed outlier: 3.583A pdb=" N GLN g 123 " --> pdb=" O SER g 119 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE g 124 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR g 129 " --> pdb=" O GLU g 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA g 131 " --> pdb=" O ALA g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 179 through 234 removed outlier: 4.186A pdb=" N GLY g 188 " --> pdb=" O LYS g 184 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR g 189 " --> pdb=" O THR g 185 " (cutoff:3.500A) Processing helix chain 'g' and resid 236 through 264 removed outlier: 4.199A pdb=" N ALA g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS g 243 " --> pdb=" O LYS g 239 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER g 264 " --> pdb=" O ILE g 260 " (cutoff:3.500A) Processing helix chain 'g' and resid 265 through 272 removed outlier: 4.419A pdb=" N LEU g 269 " --> pdb=" O SER g 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 149 Processing sheet with id=AA4, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 149 Processing sheet with id=AA6, first strand: chain 'F' and resid 145 through 149 Processing sheet with id=AA7, first strand: chain 'G' and resid 145 through 149 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 149 Processing sheet with id=AA9, first strand: chain 'I' and resid 145 through 149 Processing sheet with id=AB1, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AB2, first strand: chain 'K' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 146 Processing sheet with id=AB4, first strand: chain 'M' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'N' and resid 148 through 149 Processing sheet with id=AB6, first strand: chain 'O' and resid 145 through 149 Processing sheet with id=AB7, first strand: chain 'P' and resid 145 through 149 Processing sheet with id=AB8, first strand: chain 'Q' and resid 145 through 149 Processing sheet with id=AB9, first strand: chain 'R' and resid 145 through 149 removed outlier: 3.525A pdb=" N PHE R 148 " --> pdb=" O PHE R 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 145 through 149 Processing sheet with id=AC2, first strand: chain 'T' and resid 145 through 149 Processing sheet with id=AC3, first strand: chain 'U' and resid 145 through 149 Processing sheet with id=AC4, first strand: chain 'V' and resid 145 through 149 removed outlier: 3.545A pdb=" N PHE V 148 " --> pdb=" O PHE V 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'X' and resid 145 through 149 removed outlier: 3.531A pdb=" N PHE X 148 " --> pdb=" O PHE X 157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 145 through 149 Processing sheet with id=AC8, first strand: chain 'Z' and resid 145 through 149 Processing sheet with id=AC9, first strand: chain 'a' and resid 145 through 149 Processing sheet with id=AD1, first strand: chain 'b' and resid 145 through 149 removed outlier: 3.511A pdb=" N PHE b 148 " --> pdb=" O PHE b 157 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 145 through 149 removed outlier: 3.589A pdb=" N PHE c 148 " --> pdb=" O PHE c 157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 145 through 146 Processing sheet with id=AD4, first strand: chain 'e' and resid 145 through 146 Processing sheet with id=AD5, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AD6, first strand: chain 'j' and resid 145 through 146 Processing sheet with id=AD7, first strand: chain 'g' and resid 145 through 149 removed outlier: 3.697A pdb=" N PHE g 148 " --> pdb=" O PHE g 157 " (cutoff:3.500A) 6174 hydrogen bonds defined for protein. 18174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.17 Time building geometry restraints manager: 16.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 18509 1.33 - 1.45: 10247 1.45 - 1.57: 41012 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 70056 Sorted by residual: bond pdb=" N LEU f 90 " pdb=" CA LEU f 90 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" N LEU E 204 " pdb=" CA LEU E 204 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 bond pdb=" CA ASN g 4 " pdb=" CB ASN g 4 " ideal model delta sigma weight residual 1.527 1.543 -0.016 7.60e-03 1.73e+04 4.19e+00 bond pdb=" CG1 ILE R 190 " pdb=" CD1 ILE R 190 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 bond pdb=" CG1 ILE i 124 " pdb=" CD1 ILE i 124 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 ... (remaining 70051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 93665 2.02 - 4.05: 1011 4.05 - 6.07: 120 6.07 - 8.09: 16 8.09 - 10.12: 12 Bond angle restraints: 94824 Sorted by residual: angle pdb=" N ILE X 164 " pdb=" CA ILE X 164 " pdb=" C ILE X 164 " ideal model delta sigma weight residual 112.43 109.39 3.04 9.20e-01 1.18e+00 1.09e+01 angle pdb=" N GLN Q 31 " pdb=" CA GLN Q 31 " pdb=" CB GLN Q 31 " ideal model delta sigma weight residual 110.12 114.94 -4.82 1.47e+00 4.63e-01 1.08e+01 angle pdb=" N GLN K 31 " pdb=" CA GLN K 31 " pdb=" CB GLN K 31 " ideal model delta sigma weight residual 110.16 114.91 -4.75 1.48e+00 4.57e-01 1.03e+01 angle pdb=" CB MET h 93 " pdb=" CG MET h 93 " pdb=" SD MET h 93 " ideal model delta sigma weight residual 112.70 103.12 9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta sigma weight residual 110.28 115.20 -4.92 1.55e+00 4.16e-01 1.01e+01 ... (remaining 94819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 40057 17.95 - 35.90: 2236 35.90 - 53.86: 243 53.86 - 71.81: 78 71.81 - 89.76: 82 Dihedral angle restraints: 42696 sinusoidal: 15012 harmonic: 27684 Sorted by residual: dihedral pdb=" CA THR g 103 " pdb=" C THR g 103 " pdb=" N SER g 104 " pdb=" CA SER g 104 " ideal model delta harmonic sigma weight residual 180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA LEU Y 232 " pdb=" C LEU Y 232 " pdb=" N VAL Y 233 " pdb=" CA VAL Y 233 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP g 118 " pdb=" CB ASP g 118 " pdb=" CG ASP g 118 " pdb=" OD1 ASP g 118 " ideal model delta sinusoidal sigma weight residual -30.00 -90.33 60.33 1 2.00e+01 2.50e-03 1.21e+01 ... (remaining 42693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 10687 0.055 - 0.111: 1385 0.111 - 0.166: 128 0.166 - 0.222: 2 0.222 - 0.277: 2 Chirality restraints: 12204 Sorted by residual: chirality pdb=" CB ILE e 86 " pdb=" CA ILE e 86 " pdb=" CG1 ILE e 86 " pdb=" CG2 ILE e 86 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE g 164 " pdb=" CA ILE g 164 " pdb=" CG1 ILE g 164 " pdb=" CG2 ILE g 164 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU W 89 " pdb=" CB LEU W 89 " pdb=" CD1 LEU W 89 " pdb=" CD2 LEU W 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 12201 not shown) Planarity restraints: 12132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA e 82 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ALA e 82 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA e 82 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY e 83 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 84 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" CG ASP L 84 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP L 84 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP L 84 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 77 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" CG ASP L 77 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP L 77 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP L 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 12129 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 700 2.64 - 3.20: 68775 3.20 - 3.77: 112585 3.77 - 4.33: 145255 4.33 - 4.90: 246371 Nonbonded interactions: 573686 Sorted by model distance: nonbonded pdb=" O ILE C 6 " pdb=" OG SER j 246 " model vdw 2.072 3.040 nonbonded pdb=" NH2 ARG Z 71 " pdb=" OD2 ASP a 102 " model vdw 2.108 3.120 nonbonded pdb=" NH1 ARG O 121 " pdb=" O THR O 173 " model vdw 2.126 3.120 nonbonded pdb=" O ILE i 6 " pdb=" OG SER g 246 " model vdw 2.131 3.040 nonbonded pdb=" OG SER f 246 " pdb=" O ILE h 6 " model vdw 2.132 3.040 ... (remaining 573681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.080 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 113.790 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.820 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 70056 Z= 0.222 Angle : 0.571 10.117 94824 Z= 0.324 Chirality : 0.036 0.277 12204 Planarity : 0.003 0.050 12132 Dihedral : 11.933 89.761 24696 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.08), residues: 9648 helix: 2.42 (0.06), residues: 7056 sheet: -2.68 (0.22), residues: 360 loop : 0.81 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 49 HIS 0.006 0.001 HIS Y 214 PHE 0.025 0.002 PHE b 217 ARG 0.009 0.001 ARG W 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1069 time to evaluate : 5.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7718 (mt0) cc_final: 0.7317 (tm-30) REVERT: B 126 LYS cc_start: 0.7202 (mmmm) cc_final: 0.6702 (mppt) REVERT: B 240 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 67 ASP cc_start: 0.7687 (m-30) cc_final: 0.7385 (m-30) REVERT: C 125 GLU cc_start: 0.8118 (tp30) cc_final: 0.7800 (tp30) REVERT: C 191 ASP cc_start: 0.8331 (t0) cc_final: 0.8064 (t70) REVERT: E 88 ASP cc_start: 0.7740 (m-30) cc_final: 0.7400 (m-30) REVERT: G 62 MET cc_start: 0.8489 (mmt) cc_final: 0.8238 (mmt) REVERT: H 95 GLU cc_start: 0.8345 (tt0) cc_final: 0.8075 (tt0) REVERT: I 236 ASP cc_start: 0.7367 (t0) cc_final: 0.7105 (t70) REVERT: L 206 THR cc_start: 0.7713 (t) cc_final: 0.7408 (m) REVERT: M 38 LYS cc_start: 0.7274 (ptmt) cc_final: 0.6738 (pttm) REVERT: O 9 ASN cc_start: 0.8539 (t0) cc_final: 0.8209 (t0) REVERT: P 88 ASP cc_start: 0.7071 (p0) cc_final: 0.6859 (m-30) REVERT: P 118 ASP cc_start: 0.7784 (m-30) cc_final: 0.7174 (m-30) REVERT: P 263 GLN cc_start: 0.7634 (mp10) cc_final: 0.7417 (mp10) REVERT: Q 43 LYS cc_start: 0.6734 (mptt) cc_final: 0.6508 (mtpt) REVERT: R 29 VAL cc_start: 0.7820 (t) cc_final: 0.7605 (p) REVERT: R 122 ASP cc_start: 0.7193 (m-30) cc_final: 0.6882 (m-30) REVERT: R 226 ASP cc_start: 0.8340 (m-30) cc_final: 0.7991 (m-30) REVERT: R 255 VAL cc_start: 0.7680 (p) cc_final: 0.7390 (t) REVERT: T 93 MET cc_start: 0.8085 (mtp) cc_final: 0.7855 (mtp) REVERT: T 122 ASP cc_start: 0.7810 (m-30) cc_final: 0.7496 (m-30) REVERT: T 151 ASN cc_start: 0.8173 (t0) cc_final: 0.7909 (t0) REVERT: U 38 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7232 (tttm) REVERT: V 77 ASP cc_start: 0.7816 (m-30) cc_final: 0.7453 (m-30) REVERT: V 151 ASN cc_start: 0.8276 (m110) cc_final: 0.7945 (t0) REVERT: W 245 GLN cc_start: 0.6779 (mp10) cc_final: 0.5752 (mm110) REVERT: X 95 GLU cc_start: 0.6462 (tt0) cc_final: 0.6133 (tt0) REVERT: X 252 GLN cc_start: 0.7310 (tp-100) cc_final: 0.6909 (mt0) REVERT: X 256 GLN cc_start: 0.6904 (tp-100) cc_final: 0.6200 (pt0) REVERT: Y 88 ASP cc_start: 0.8279 (m-30) cc_final: 0.8077 (m-30) REVERT: Y 122 ASP cc_start: 0.8643 (m-30) cc_final: 0.8422 (m-30) REVERT: Z 116 ASP cc_start: 0.7599 (m-30) cc_final: 0.7388 (m-30) REVERT: Z 256 GLN cc_start: 0.7656 (mm110) cc_final: 0.7296 (mt0) REVERT: a 95 GLU cc_start: 0.8189 (tt0) cc_final: 0.7968 (tt0) REVERT: a 240 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6606 (mm-30) REVERT: b 134 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7315 (t0) REVERT: c 95 GLU cc_start: 0.7990 (tp30) cc_final: 0.7781 (tt0) REVERT: d 256 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7536 (mt0) REVERT: e 31 GLN cc_start: 0.7180 (pp30) cc_final: 0.6443 (mm110) REVERT: e 105 LEU cc_start: 0.7950 (mt) cc_final: 0.7578 (mt) REVERT: g 9 ASN cc_start: 0.7420 (t0) cc_final: 0.7212 (t0) REVERT: g 25 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6493 (mt-10) REVERT: g 106 ASN cc_start: 0.3446 (t0) cc_final: 0.3142 (p0) outliers start: 3 outliers final: 5 residues processed: 1071 average time/residue: 1.3864 time to fit residues: 1963.7773 Evaluate side-chains 583 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 577 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 45 ASN Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 134 ASN Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain i residue 84 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 4.9990 chunk 736 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 496 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 chunk 761 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 463 optimal weight: 10.0000 chunk 567 optimal weight: 1.9990 chunk 882 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN B 18 ASN D 251 GLN E 70 GLN E 123 GLN E 151 ASN E 245 GLN E 252 GLN F 31 GLN F 245 GLN F 256 GLN F 263 GLN G 23 ASN G 251 GLN H 4 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 23 ASN I 130 ASN I 251 GLN J 9 ASN J 20 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 ASN K 252 GLN K 262 ASN L 7 ASN L 130 ASN L 134 ASN L 199 ASN L 231 ASN M 20 ASN M 130 ASN O 4 ASN P 4 ASN P 55 GLN Q 7 ASN Q 111 ASN Q 130 ASN Q 262 ASN R 23 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN S 151 ASN T 7 ASN T 9 ASN T 63 ASN T 123 GLN U 31 GLN U 130 ASN V 30 GLN V 31 GLN V 252 GLN W 23 ASN W 30 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 251 GLN X 4 ASN X 248 GLN Y 195 GLN Y 222 GLN Y 262 ASN Z 123 GLN Z 130 ASN Z 262 ASN ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 199 ASN a 245 GLN b 18 ASN b 248 GLN b 263 GLN c 45 ASN c 55 GLN c 123 GLN d 30 GLN e 18 ASN f 7 ASN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 111 ASN f 245 GLN h 18 ASN ** h 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 262 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 GLN ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 GLN j 18 ASN g 73 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111590 restraints weight = 110704.713| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.58 r_work: 0.3493 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 70056 Z= 0.263 Angle : 0.523 8.663 94824 Z= 0.293 Chirality : 0.036 0.209 12204 Planarity : 0.003 0.033 12132 Dihedral : 4.000 72.525 9804 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.01 % Allowed : 7.17 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.08), residues: 9648 helix: 3.18 (0.06), residues: 6804 sheet: -2.51 (0.22), residues: 360 loop : 1.37 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 49 HIS 0.005 0.002 HIS J 214 PHE 0.018 0.002 PHE T 110 ARG 0.008 0.001 ARG H 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 631 time to evaluate : 5.860 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7991 (mt0) cc_final: 0.7783 (tm-30) REVERT: B 126 LYS cc_start: 0.7950 (mmmm) cc_final: 0.7626 (mtmt) REVERT: B 240 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 67 ASP cc_start: 0.8036 (m-30) cc_final: 0.7768 (m-30) REVERT: C 191 ASP cc_start: 0.8867 (t0) cc_final: 0.8606 (t0) REVERT: C 256 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: D 212 ASP cc_start: 0.8571 (t70) cc_final: 0.8362 (m-30) REVERT: E 31 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7401 (mt0) REVERT: E 88 ASP cc_start: 0.7909 (m-30) cc_final: 0.7530 (m-30) REVERT: E 95 GLU cc_start: 0.5670 (mm-30) cc_final: 0.5344 (mm-30) REVERT: F 251 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: F 252 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8579 (mm-40) REVERT: G 240 GLU cc_start: 0.8218 (mp0) cc_final: 0.7979 (mp0) REVERT: K 195 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: L 206 THR cc_start: 0.7679 (t) cc_final: 0.7324 (m) REVERT: M 38 LYS cc_start: 0.7611 (ptmt) cc_final: 0.7088 (pttm) REVERT: N 31 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: P 118 ASP cc_start: 0.8021 (m-30) cc_final: 0.7680 (m-30) REVERT: Q 43 LYS cc_start: 0.6894 (mptt) cc_final: 0.6541 (mtpt) REVERT: R 122 ASP cc_start: 0.7566 (m-30) cc_final: 0.7326 (m-30) REVERT: R 220 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.4493 (mtpt) REVERT: R 226 ASP cc_start: 0.8430 (m-30) cc_final: 0.8129 (m-30) REVERT: R 255 VAL cc_start: 0.8080 (p) cc_final: 0.7788 (t) REVERT: S 31 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7494 (tp40) REVERT: T 31 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: T 95 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: T 118 ASP cc_start: 0.8039 (m-30) cc_final: 0.7643 (m-30) REVERT: T 122 ASP cc_start: 0.8014 (m-30) cc_final: 0.7810 (m-30) REVERT: U 31 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.6899 (tp40) REVERT: U 93 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8027 (mtt) REVERT: V 77 ASP cc_start: 0.7765 (m-30) cc_final: 0.7543 (m-30) REVERT: W 6 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7049 (tt) REVERT: W 245 GLN cc_start: 0.7152 (mp10) cc_final: 0.6674 (mm-40) REVERT: X 95 GLU cc_start: 0.6858 (tt0) cc_final: 0.6467 (tt0) REVERT: X 256 GLN cc_start: 0.7045 (tp-100) cc_final: 0.6589 (pt0) REVERT: Z 256 GLN cc_start: 0.7731 (mm110) cc_final: 0.7386 (mt0) REVERT: Z 263 GLN cc_start: 0.7838 (mp10) cc_final: 0.7476 (mp10) REVERT: a 240 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6818 (mm-30) REVERT: a 262 ASN cc_start: 0.7220 (t0) cc_final: 0.6959 (m-40) REVERT: c 93 MET cc_start: 0.8300 (ttm) cc_final: 0.8094 (mtp) REVERT: c 256 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: d 256 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7815 (mt0) REVERT: e 31 GLN cc_start: 0.7354 (pp30) cc_final: 0.6482 (mm110) REVERT: e 105 LEU cc_start: 0.7964 (mt) cc_final: 0.7607 (mt) REVERT: f 95 GLU cc_start: 0.5796 (tp30) cc_final: 0.5509 (tt0) REVERT: h 71 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7606 (ttp-110) REVERT: h 144 THR cc_start: 0.8696 (t) cc_final: 0.8302 (m) REVERT: g 25 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6439 (mt-10) REVERT: g 145 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7511 (ptmm) outliers start: 152 outliers final: 64 residues processed: 744 average time/residue: 1.3370 time to fit residues: 1331.6180 Evaluate side-chains 622 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 545 time to evaluate : 5.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 251 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 123 GLN Chi-restraints excluded: chain P residue 122 ASP Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 178 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain c residue 256 GLN Chi-restraints excluded: chain e residue 117 PHE Chi-restraints excluded: chain e residue 147 THR Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 145 LYS Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 99 optimal weight: 3.9990 chunk 414 optimal weight: 0.8980 chunk 916 optimal weight: 0.7980 chunk 385 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 849 optimal weight: 2.9990 chunk 808 optimal weight: 2.9990 chunk 724 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN C 7 ASN D 130 ASN E 123 GLN E 130 ASN F 31 GLN F 256 GLN F 263 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN L 199 ASN M 123 GLN O 4 ASN O 199 ASN Q 70 GLN R 263 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 248 GLN T 123 GLN U 18 ASN U 130 ASN U 262 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 55 GLN X 252 GLN Y 151 ASN Z 130 ASN Z 151 ASN a 20 ASN a 245 GLN b 245 GLN c 45 ASN c 55 GLN c 195 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 54 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 7 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113030 restraints weight = 110602.643| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.58 r_work: 0.3512 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 70056 Z= 0.197 Angle : 0.447 7.571 94824 Z= 0.256 Chirality : 0.033 0.199 12204 Planarity : 0.002 0.041 12132 Dihedral : 3.694 25.314 9794 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.12 % Allowed : 8.43 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.08), residues: 9648 helix: 3.52 (0.06), residues: 6804 sheet: -2.24 (0.23), residues: 360 loop : 1.19 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 49 HIS 0.004 0.001 HIS J 214 PHE 0.014 0.002 PHE b 117 ARG 0.007 0.000 ARG g 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 617 time to evaluate : 6.451 Fit side-chains REVERT: A 13 MET cc_start: 0.8162 (mtm) cc_final: 0.7954 (mtt) REVERT: A 31 GLN cc_start: 0.7953 (mt0) cc_final: 0.7736 (tm-30) REVERT: B 126 LYS cc_start: 0.7902 (mmmm) cc_final: 0.7577 (mtmt) REVERT: B 240 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 252 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: C 67 ASP cc_start: 0.7996 (m-30) cc_final: 0.7753 (m-30) REVERT: C 191 ASP cc_start: 0.8791 (t0) cc_final: 0.8548 (t0) REVERT: C 256 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: D 20 ASN cc_start: 0.8289 (m110) cc_final: 0.7953 (m110) REVERT: D 212 ASP cc_start: 0.8532 (t70) cc_final: 0.8311 (m-30) REVERT: E 88 ASP cc_start: 0.7930 (m-30) cc_final: 0.7548 (m-30) REVERT: E 220 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6904 (mmtt) REVERT: F 251 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: F 252 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8593 (mm-40) REVERT: J 45 ASN cc_start: 0.8919 (t0) cc_final: 0.8652 (t0) REVERT: K 195 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: L 95 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6436 (tt0) REVERT: L 206 THR cc_start: 0.7741 (t) cc_final: 0.7393 (m) REVERT: M 38 LYS cc_start: 0.7582 (ptmt) cc_final: 0.7080 (pttm) REVERT: P 245 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6319 (mp10) REVERT: Q 43 LYS cc_start: 0.6919 (mptt) cc_final: 0.6538 (mtpt) REVERT: Q 176 THR cc_start: 0.8017 (t) cc_final: 0.7477 (m) REVERT: Q 263 GLN cc_start: 0.7913 (mp10) cc_final: 0.6708 (pp30) REVERT: R 122 ASP cc_start: 0.7503 (m-30) cc_final: 0.7253 (m-30) REVERT: R 226 ASP cc_start: 0.8372 (m-30) cc_final: 0.8079 (m-30) REVERT: R 255 VAL cc_start: 0.8035 (p) cc_final: 0.7767 (t) REVERT: S 256 GLN cc_start: 0.8282 (tt0) cc_final: 0.8052 (mt0) REVERT: T 31 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: T 95 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: T 118 ASP cc_start: 0.8050 (m-30) cc_final: 0.7654 (m-30) REVERT: U 31 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7552 (tp-100) REVERT: U 93 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7773 (mtt) REVERT: V 77 ASP cc_start: 0.7726 (m-30) cc_final: 0.7477 (m-30) REVERT: W 245 GLN cc_start: 0.7200 (mp10) cc_final: 0.6780 (mm-40) REVERT: X 95 GLU cc_start: 0.6818 (tt0) cc_final: 0.6496 (tt0) REVERT: X 256 GLN cc_start: 0.7048 (tp-100) cc_final: 0.6481 (pt0) REVERT: Z 256 GLN cc_start: 0.7721 (mm110) cc_final: 0.7374 (mt0) REVERT: a 151 ASN cc_start: 0.8421 (t0) cc_final: 0.7994 (t0) REVERT: a 262 ASN cc_start: 0.7317 (t0) cc_final: 0.7107 (m-40) REVERT: b 32 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6385 (ttp-170) REVERT: c 93 MET cc_start: 0.8231 (ttm) cc_final: 0.8027 (mtp) REVERT: d 31 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: d 256 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7798 (mt0) REVERT: e 31 GLN cc_start: 0.7285 (pp30) cc_final: 0.6343 (mm110) REVERT: e 105 LEU cc_start: 0.7911 (mt) cc_final: 0.7554 (mt) REVERT: h 144 THR cc_start: 0.8703 (t) cc_final: 0.8314 (m) REVERT: g 25 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6364 (mt-10) outliers start: 160 outliers final: 65 residues processed: 726 average time/residue: 1.3330 time to fit residues: 1301.4130 Evaluate side-chains 630 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 553 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 251 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 264 SER Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 258 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain j residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 138 ILE Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 401 optimal weight: 3.9990 chunk 675 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 490 optimal weight: 3.9990 chunk 713 optimal weight: 0.9980 chunk 885 optimal weight: 0.9980 chunk 883 optimal weight: 5.9990 chunk 682 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN D 23 ASN E 231 ASN F 31 GLN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN H 45 ASN I 195 GLN I 199 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 199 ASN M 4 ASN O 130 ASN P 130 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 31 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN V 252 GLN X 252 GLN Z 151 ASN a 245 GLN b 245 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 262 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112188 restraints weight = 110907.053| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.58 r_work: 0.3499 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 70056 Z= 0.209 Angle : 0.445 9.290 94824 Z= 0.254 Chirality : 0.034 0.183 12204 Planarity : 0.002 0.041 12132 Dihedral : 3.656 25.282 9794 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.24 % Allowed : 9.51 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.08), residues: 9648 helix: 3.60 (0.06), residues: 6804 sheet: -2.10 (0.24), residues: 360 loop : 1.06 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 49 HIS 0.004 0.001 HIS J 214 PHE 0.016 0.002 PHE b 117 ARG 0.009 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 598 time to evaluate : 5.811 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.8112 (mtm) cc_final: 0.7905 (mtt) REVERT: A 31 GLN cc_start: 0.7986 (mt0) cc_final: 0.7750 (tm-30) REVERT: B 126 LYS cc_start: 0.7942 (mmmm) cc_final: 0.7576 (mtmt) REVERT: B 240 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 252 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: C 67 ASP cc_start: 0.7976 (m-30) cc_final: 0.7712 (m-30) REVERT: C 191 ASP cc_start: 0.8833 (t0) cc_final: 0.8599 (t0) REVERT: C 256 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: D 20 ASN cc_start: 0.8277 (m110) cc_final: 0.7902 (m110) REVERT: D 212 ASP cc_start: 0.8529 (t70) cc_final: 0.8282 (m-30) REVERT: E 88 ASP cc_start: 0.7936 (m-30) cc_final: 0.7556 (m-30) REVERT: E 220 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6899 (mmtt) REVERT: H 98 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6561 (tt) REVERT: J 45 ASN cc_start: 0.8906 (t0) cc_final: 0.8623 (t0) REVERT: K 195 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: L 206 THR cc_start: 0.7798 (t) cc_final: 0.7427 (m) REVERT: M 38 LYS cc_start: 0.7615 (ptmt) cc_final: 0.7089 (pttm) REVERT: N 31 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: P 9 ASN cc_start: 0.7823 (t0) cc_final: 0.7531 (t0) REVERT: P 245 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6302 (mp10) REVERT: Q 43 LYS cc_start: 0.6866 (mptt) cc_final: 0.6418 (mtpt) REVERT: Q 93 MET cc_start: 0.6383 (mtp) cc_final: 0.6136 (mtm) REVERT: Q 176 THR cc_start: 0.7932 (t) cc_final: 0.7522 (m) REVERT: R 122 ASP cc_start: 0.7536 (m-30) cc_final: 0.7294 (m-30) REVERT: R 220 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.4342 (mtpt) REVERT: R 226 ASP cc_start: 0.8387 (m-30) cc_final: 0.8107 (m-30) REVERT: R 255 VAL cc_start: 0.8072 (p) cc_final: 0.7798 (t) REVERT: S 256 GLN cc_start: 0.8358 (tt0) cc_final: 0.8076 (mt0) REVERT: T 95 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: T 245 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: U 93 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: V 77 ASP cc_start: 0.7750 (m-30) cc_final: 0.7503 (m-30) REVERT: X 90 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7643 (tp) REVERT: X 95 GLU cc_start: 0.6698 (tt0) cc_final: 0.6347 (tt0) REVERT: Z 256 GLN cc_start: 0.7728 (mm110) cc_final: 0.7390 (mt0) REVERT: a 151 ASN cc_start: 0.8382 (t0) cc_final: 0.7963 (t0) REVERT: b 32 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.5980 (ttp-170) REVERT: b 105 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6710 (pp) REVERT: b 240 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7430 (mm-30) REVERT: c 93 MET cc_start: 0.8247 (ttm) cc_final: 0.8038 (mtp) REVERT: c 195 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6847 (mm110) REVERT: d 31 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: d 245 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: d 256 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7793 (mt0) REVERT: e 31 GLN cc_start: 0.7300 (pp30) cc_final: 0.6270 (mm-40) REVERT: e 105 LEU cc_start: 0.7925 (mt) cc_final: 0.7561 (mt) REVERT: h 144 THR cc_start: 0.8668 (t) cc_final: 0.8304 (m) REVERT: h 263 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7897 (mm110) REVERT: i 84 ASP cc_start: 0.6977 (t0) cc_final: 0.6427 (t0) REVERT: g 25 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6437 (mt-10) REVERT: g 145 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7577 (ptmm) outliers start: 169 outliers final: 80 residues processed: 725 average time/residue: 1.2893 time to fit residues: 1262.7799 Evaluate side-chains 652 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 554 time to evaluate : 5.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 123 GLN Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 245 GLN Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain d residue 258 LEU Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 204 LEU Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 33 ILE Chi-restraints excluded: chain j residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 145 LYS Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 526 optimal weight: 10.0000 chunk 901 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 283 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 chunk 853 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 858 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 542 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN P 130 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Y 151 ASN Z 151 ASN Z 231 ASN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN d 73 GLN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 18 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112568 restraints weight = 110726.167| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.58 r_work: 0.3503 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 70056 Z= 0.196 Angle : 0.433 8.438 94824 Z= 0.248 Chirality : 0.033 0.238 12204 Planarity : 0.002 0.041 12132 Dihedral : 3.602 25.328 9794 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.16 % Allowed : 10.29 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.08), residues: 9648 helix: 3.69 (0.06), residues: 6804 sheet: -1.89 (0.24), residues: 360 loop : 0.96 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.027 0.002 PHE Q 117 ARG 0.008 0.000 ARG g 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 600 time to evaluate : 5.829 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.8093 (mtm) cc_final: 0.7888 (mtt) REVERT: A 31 GLN cc_start: 0.7975 (mt0) cc_final: 0.7773 (tm-30) REVERT: B 126 LYS cc_start: 0.7931 (mmmm) cc_final: 0.7562 (mtmt) REVERT: B 240 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 252 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: C 67 ASP cc_start: 0.7986 (m-30) cc_final: 0.7717 (m-30) REVERT: C 191 ASP cc_start: 0.8825 (t0) cc_final: 0.8592 (t0) REVERT: C 256 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: D 20 ASN cc_start: 0.8301 (m110) cc_final: 0.7907 (m110) REVERT: D 212 ASP cc_start: 0.8524 (t70) cc_final: 0.8277 (m-30) REVERT: E 88 ASP cc_start: 0.7980 (m-30) cc_final: 0.7608 (m-30) REVERT: E 95 GLU cc_start: 0.6263 (mm-30) cc_final: 0.6040 (mm-30) REVERT: E 220 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6902 (mmtt) REVERT: H 98 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6461 (tt) REVERT: H 171 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7392 (mm) REVERT: J 45 ASN cc_start: 0.8902 (t0) cc_final: 0.8585 (t0) REVERT: K 195 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: K 243 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7754 (mmtt) REVERT: L 95 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6326 (tt0) REVERT: L 206 THR cc_start: 0.7795 (t) cc_final: 0.7421 (m) REVERT: M 38 LYS cc_start: 0.7568 (ptmt) cc_final: 0.7077 (pttm) REVERT: N 31 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: P 9 ASN cc_start: 0.7858 (t0) cc_final: 0.7553 (t0) REVERT: P 118 ASP cc_start: 0.7906 (m-30) cc_final: 0.7633 (m-30) REVERT: P 245 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6240 (mp10) REVERT: Q 43 LYS cc_start: 0.6893 (mptt) cc_final: 0.6410 (mtpt) REVERT: Q 176 THR cc_start: 0.7962 (t) cc_final: 0.7516 (m) REVERT: Q 253 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7889 (tt) REVERT: R 67 ASP cc_start: 0.7754 (m-30) cc_final: 0.7231 (t0) REVERT: R 122 ASP cc_start: 0.7525 (m-30) cc_final: 0.7286 (m-30) REVERT: R 220 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.4308 (mtpt) REVERT: R 226 ASP cc_start: 0.8375 (m-30) cc_final: 0.8087 (m-30) REVERT: R 255 VAL cc_start: 0.8053 (p) cc_final: 0.7796 (t) REVERT: S 256 GLN cc_start: 0.8399 (tt0) cc_final: 0.8065 (mt0) REVERT: T 95 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: T 245 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: U 93 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7755 (mtt) REVERT: V 77 ASP cc_start: 0.7740 (m-30) cc_final: 0.7502 (m-30) REVERT: X 90 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7629 (tp) REVERT: X 95 GLU cc_start: 0.6719 (tt0) cc_final: 0.6389 (tt0) REVERT: Z 256 GLN cc_start: 0.7725 (mm110) cc_final: 0.7394 (mt0) REVERT: a 151 ASN cc_start: 0.8406 (t0) cc_final: 0.7969 (t0) REVERT: b 32 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6072 (ttp-170) REVERT: b 62 MET cc_start: 0.8347 (mmt) cc_final: 0.7801 (mmt) REVERT: b 105 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6743 (pp) REVERT: b 240 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7489 (mm-30) REVERT: c 93 MET cc_start: 0.8231 (ttm) cc_final: 0.8020 (mtp) REVERT: c 195 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6853 (mm110) REVERT: d 31 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: d 245 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: d 256 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7793 (mt0) REVERT: e 31 GLN cc_start: 0.7282 (pp30) cc_final: 0.6241 (mm-40) REVERT: e 105 LEU cc_start: 0.7898 (mt) cc_final: 0.7559 (mt) REVERT: f 95 GLU cc_start: 0.5756 (tp30) cc_final: 0.5551 (tt0) REVERT: f 263 GLN cc_start: 0.7362 (tp-100) cc_final: 0.6733 (mt0) REVERT: h 144 THR cc_start: 0.8674 (t) cc_final: 0.8310 (m) REVERT: h 263 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7921 (mm110) REVERT: g 25 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6387 (mt-10) REVERT: g 123 GLN cc_start: 0.4756 (mp10) cc_final: 0.4081 (mm-40) outliers start: 163 outliers final: 81 residues processed: 716 average time/residue: 1.2895 time to fit residues: 1245.8613 Evaluate side-chains 663 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 562 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 123 GLN Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 245 GLN Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 204 LEU Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 465 optimal weight: 1.9990 chunk 456 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 542 optimal weight: 3.9990 chunk 822 optimal weight: 0.9980 chunk 368 optimal weight: 0.0050 chunk 174 optimal weight: 4.9990 chunk 828 optimal weight: 0.9990 chunk 671 optimal weight: 5.9990 chunk 654 optimal weight: 2.9990 chunk 731 optimal weight: 3.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN I 199 ASN I 231 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN X 263 GLN Z 30 GLN Z 151 ASN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 256 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113880 restraints weight = 110062.141| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.58 r_work: 0.3521 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 70056 Z= 0.172 Angle : 0.415 9.847 94824 Z= 0.238 Chirality : 0.032 0.193 12204 Planarity : 0.002 0.030 12132 Dihedral : 3.521 25.190 9794 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.02 % Allowed : 10.81 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.08), residues: 9648 helix: 3.80 (0.06), residues: 6804 sheet: -1.72 (0.24), residues: 360 loop : 0.95 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.017 0.001 PHE R 110 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 611 time to evaluate : 5.930 Fit side-chains REVERT: A 31 GLN cc_start: 0.7944 (mt0) cc_final: 0.7716 (tm-30) REVERT: B 126 LYS cc_start: 0.7884 (mmmm) cc_final: 0.7513 (mtmt) REVERT: B 240 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7674 (mm-30) REVERT: B 252 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: C 67 ASP cc_start: 0.7998 (m-30) cc_final: 0.7765 (m-30) REVERT: C 191 ASP cc_start: 0.8803 (t0) cc_final: 0.8575 (t0) REVERT: D 20 ASN cc_start: 0.8287 (m110) cc_final: 0.7884 (m110) REVERT: D 212 ASP cc_start: 0.8507 (t70) cc_final: 0.8260 (m-30) REVERT: E 31 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7274 (mt0) REVERT: E 84 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: E 88 ASP cc_start: 0.7961 (m-30) cc_final: 0.7590 (m-30) REVERT: E 177 PHE cc_start: 0.7185 (p90) cc_final: 0.6944 (p90) REVERT: E 220 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6829 (mmtt) REVERT: H 98 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6393 (tt) REVERT: H 171 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7390 (mm) REVERT: J 45 ASN cc_start: 0.8848 (t0) cc_final: 0.8524 (t0) REVERT: J 77 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: K 195 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: K 243 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7751 (mmtt) REVERT: L 95 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6405 (tt0) REVERT: L 206 THR cc_start: 0.7741 (t) cc_final: 0.7365 (m) REVERT: M 38 LYS cc_start: 0.7556 (ptmt) cc_final: 0.7109 (pttm) REVERT: N 31 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6626 (mp10) REVERT: P 9 ASN cc_start: 0.7883 (t0) cc_final: 0.7576 (t0) REVERT: P 122 ASP cc_start: 0.7122 (p0) cc_final: 0.6712 (t0) REVERT: P 245 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6212 (mp10) REVERT: Q 43 LYS cc_start: 0.6872 (mptt) cc_final: 0.6368 (mtpt) REVERT: Q 176 THR cc_start: 0.7954 (t) cc_final: 0.7568 (m) REVERT: R 67 ASP cc_start: 0.7722 (m-30) cc_final: 0.7206 (t0) REVERT: R 122 ASP cc_start: 0.7492 (m-30) cc_final: 0.7249 (m-30) REVERT: R 226 ASP cc_start: 0.8337 (m-30) cc_final: 0.8058 (m-30) REVERT: R 255 VAL cc_start: 0.8040 (p) cc_final: 0.7793 (t) REVERT: S 31 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7442 (tp40) REVERT: S 256 GLN cc_start: 0.8394 (tt0) cc_final: 0.8079 (mt0) REVERT: T 31 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: T 95 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: T 245 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: U 93 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7608 (mtt) REVERT: V 77 ASP cc_start: 0.7727 (m-30) cc_final: 0.7517 (m-30) REVERT: X 90 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7576 (tp) REVERT: X 95 GLU cc_start: 0.6800 (tt0) cc_final: 0.6490 (tt0) REVERT: Z 116 ASP cc_start: 0.7935 (m-30) cc_final: 0.7576 (m-30) REVERT: Z 256 GLN cc_start: 0.7722 (mm110) cc_final: 0.7383 (mt0) REVERT: a 151 ASN cc_start: 0.8403 (t0) cc_final: 0.7958 (t0) REVERT: a 262 ASN cc_start: 0.7392 (t0) cc_final: 0.7169 (m-40) REVERT: b 32 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.5954 (ttp-170) REVERT: b 105 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6701 (pp) REVERT: b 240 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7479 (mm-30) REVERT: c 93 MET cc_start: 0.8255 (ttm) cc_final: 0.8049 (mtp) REVERT: c 195 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6834 (mm110) REVERT: d 31 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: d 245 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: d 256 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7753 (mt0) REVERT: e 105 LEU cc_start: 0.7938 (mt) cc_final: 0.7597 (mt) REVERT: f 263 GLN cc_start: 0.7393 (tp-100) cc_final: 0.6778 (mt0) REVERT: h 144 THR cc_start: 0.8603 (t) cc_final: 0.8233 (m) REVERT: h 263 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7889 (mm110) REVERT: i 84 ASP cc_start: 0.6961 (t0) cc_final: 0.6358 (t0) REVERT: g 25 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6409 (mt-10) REVERT: g 123 GLN cc_start: 0.4736 (mp10) cc_final: 0.4016 (mm-40) outliers start: 153 outliers final: 75 residues processed: 729 average time/residue: 1.2432 time to fit residues: 1238.2929 Evaluate side-chains 662 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 566 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 123 GLN Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 245 GLN Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 204 LEU Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 544 optimal weight: 4.9990 chunk 535 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 615 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 829 optimal weight: 0.9990 chunk 843 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 911 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 825 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN C 195 GLN F 31 GLN F 134 ASN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN J 30 GLN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 30 GLN W 34 ASN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN X 263 GLN Z 151 ASN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 7 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116170 restraints weight = 109764.038| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.58 r_work: 0.3553 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 70056 Z= 0.149 Angle : 0.395 9.521 94824 Z= 0.229 Chirality : 0.031 0.204 12204 Planarity : 0.002 0.031 12132 Dihedral : 3.420 26.819 9794 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.83 % Allowed : 11.63 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.54 (0.09), residues: 9648 helix: 3.94 (0.06), residues: 6804 sheet: -1.54 (0.24), residues: 360 loop : 0.94 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 49 HIS 0.003 0.001 HIS J 214 PHE 0.014 0.001 PHE b 117 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 626 time to evaluate : 5.941 Fit side-chains REVERT: A 31 GLN cc_start: 0.7927 (mt0) cc_final: 0.7714 (tm-30) REVERT: B 126 LYS cc_start: 0.7813 (mmmm) cc_final: 0.7534 (mtmt) REVERT: B 240 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 252 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: C 67 ASP cc_start: 0.7913 (m-30) cc_final: 0.7680 (m-30) REVERT: C 191 ASP cc_start: 0.8749 (t0) cc_final: 0.8515 (t0) REVERT: D 20 ASN cc_start: 0.8281 (m110) cc_final: 0.7892 (m110) REVERT: D 212 ASP cc_start: 0.8489 (t70) cc_final: 0.8234 (m-30) REVERT: E 31 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7255 (mt0) REVERT: E 84 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6501 (m-30) REVERT: E 88 ASP cc_start: 0.7952 (m-30) cc_final: 0.7596 (m-30) REVERT: H 98 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6133 (tt) REVERT: J 45 ASN cc_start: 0.8797 (t0) cc_final: 0.8453 (t0) REVERT: J 77 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: K 195 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: K 243 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7695 (mmtt) REVERT: L 95 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6240 (tt0) REVERT: L 206 THR cc_start: 0.7814 (t) cc_final: 0.7412 (m) REVERT: M 38 LYS cc_start: 0.7525 (ptmt) cc_final: 0.7088 (pttm) REVERT: P 9 ASN cc_start: 0.7961 (t0) cc_final: 0.7671 (t0) REVERT: P 122 ASP cc_start: 0.7122 (p0) cc_final: 0.6739 (t0) REVERT: P 245 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6239 (mp10) REVERT: Q 176 THR cc_start: 0.7914 (t) cc_final: 0.7580 (m) REVERT: R 122 ASP cc_start: 0.7470 (m-30) cc_final: 0.7226 (m-30) REVERT: R 226 ASP cc_start: 0.8275 (m-30) cc_final: 0.8008 (m-30) REVERT: R 255 VAL cc_start: 0.8018 (p) cc_final: 0.7765 (t) REVERT: S 31 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7599 (tp40) REVERT: S 256 GLN cc_start: 0.8411 (tt0) cc_final: 0.8050 (mt0) REVERT: S 263 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: V 77 ASP cc_start: 0.7669 (m-30) cc_final: 0.7468 (m-30) REVERT: X 90 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7562 (tp) REVERT: Y 124 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7071 (mt) REVERT: Z 116 ASP cc_start: 0.7802 (m-30) cc_final: 0.7478 (m-30) REVERT: Z 256 GLN cc_start: 0.7634 (mm110) cc_final: 0.7276 (mt0) REVERT: a 151 ASN cc_start: 0.8400 (t0) cc_final: 0.7966 (t0) REVERT: a 262 ASN cc_start: 0.7426 (t0) cc_final: 0.7226 (m-40) REVERT: b 32 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6278 (ttp-170) REVERT: b 105 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6595 (pp) REVERT: c 93 MET cc_start: 0.8227 (ttm) cc_final: 0.8012 (mtp) REVERT: c 195 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6828 (mm110) REVERT: d 245 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7083 (mt0) REVERT: d 256 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7756 (mt0) REVERT: e 105 LEU cc_start: 0.7912 (mt) cc_final: 0.7582 (mt) REVERT: f 263 GLN cc_start: 0.7403 (tp-100) cc_final: 0.6704 (mt0) REVERT: h 144 THR cc_start: 0.8595 (t) cc_final: 0.8222 (m) REVERT: i 84 ASP cc_start: 0.6964 (t0) cc_final: 0.6445 (t0) REVERT: g 164 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6878 (pt) outliers start: 138 outliers final: 62 residues processed: 737 average time/residue: 1.2643 time to fit residues: 1265.3254 Evaluate side-chains 643 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 565 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 263 GLN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 260 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 912 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 454 optimal weight: 3.9990 chunk 760 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 502 optimal weight: 0.0670 chunk 498 optimal weight: 4.9990 chunk 611 optimal weight: 9.9990 chunk 522 optimal weight: 0.9990 chunk 800 optimal weight: 20.0000 chunk 263 optimal weight: 4.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 231 ASN F 263 GLN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN M 30 GLN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN R 262 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN X 263 GLN Z 151 ASN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN c 45 ASN c 263 GLN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.114849 restraints weight = 110029.157| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.58 r_work: 0.3533 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 70056 Z= 0.172 Angle : 0.417 10.696 94824 Z= 0.238 Chirality : 0.032 0.183 12204 Planarity : 0.002 0.045 12132 Dihedral : 3.435 17.243 9792 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.81 % Allowed : 12.28 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.08), residues: 9648 helix: 3.89 (0.06), residues: 6804 sheet: -1.49 (0.25), residues: 360 loop : 0.91 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.018 0.001 PHE R 110 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 590 time to evaluate : 5.900 Fit side-chains REVERT: A 31 GLN cc_start: 0.7954 (mt0) cc_final: 0.7713 (tm-30) REVERT: B 126 LYS cc_start: 0.7888 (mmmm) cc_final: 0.7527 (mtmt) REVERT: B 240 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 252 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: C 67 ASP cc_start: 0.7940 (m-30) cc_final: 0.7709 (m-30) REVERT: C 191 ASP cc_start: 0.8747 (t0) cc_final: 0.8528 (t0) REVERT: D 20 ASN cc_start: 0.8314 (m110) cc_final: 0.7906 (m110) REVERT: D 212 ASP cc_start: 0.8498 (t70) cc_final: 0.8227 (m-30) REVERT: E 31 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7272 (mt0) REVERT: E 84 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: E 88 ASP cc_start: 0.7953 (m-30) cc_final: 0.7596 (m-30) REVERT: F 31 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7636 (tp-100) REVERT: H 98 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6191 (tt) REVERT: J 45 ASN cc_start: 0.8800 (t0) cc_final: 0.8483 (t0) REVERT: J 77 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: K 195 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: K 243 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7705 (mmtt) REVERT: L 95 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6364 (tt0) REVERT: L 206 THR cc_start: 0.7849 (t) cc_final: 0.7463 (m) REVERT: M 38 LYS cc_start: 0.7519 (ptmt) cc_final: 0.7079 (pttm) REVERT: P 9 ASN cc_start: 0.7922 (t0) cc_final: 0.7620 (t0) REVERT: P 122 ASP cc_start: 0.7110 (p0) cc_final: 0.6733 (t0) REVERT: P 245 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: Q 176 THR cc_start: 0.7915 (t) cc_final: 0.7563 (m) REVERT: R 122 ASP cc_start: 0.7515 (m-30) cc_final: 0.7281 (m-30) REVERT: R 226 ASP cc_start: 0.8298 (m-30) cc_final: 0.8021 (m-30) REVERT: R 255 VAL cc_start: 0.8034 (p) cc_final: 0.7791 (t) REVERT: S 191 ASP cc_start: 0.7639 (m-30) cc_final: 0.7350 (m-30) REVERT: S 263 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: V 77 ASP cc_start: 0.7717 (m-30) cc_final: 0.7510 (m-30) REVERT: X 93 MET cc_start: 0.7712 (mtp) cc_final: 0.7169 (mtm) REVERT: X 95 GLU cc_start: 0.6726 (tt0) cc_final: 0.6382 (tt0) REVERT: Z 116 ASP cc_start: 0.7831 (m-30) cc_final: 0.7491 (m-30) REVERT: Z 256 GLN cc_start: 0.7634 (mm110) cc_final: 0.7267 (mt0) REVERT: Z 263 GLN cc_start: 0.7956 (mp10) cc_final: 0.7676 (mp10) REVERT: a 151 ASN cc_start: 0.8384 (t0) cc_final: 0.7943 (t0) REVERT: a 262 ASN cc_start: 0.7431 (t0) cc_final: 0.7219 (m-40) REVERT: b 32 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6292 (ttp-170) REVERT: b 62 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8042 (mmt) REVERT: b 105 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6657 (pp) REVERT: c 93 MET cc_start: 0.8244 (ttm) cc_final: 0.8019 (mtp) REVERT: c 195 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6811 (mm110) REVERT: d 245 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7092 (mt0) REVERT: d 256 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7763 (mt0) REVERT: e 105 LEU cc_start: 0.7928 (mt) cc_final: 0.7604 (mt) REVERT: f 263 GLN cc_start: 0.7402 (tp-100) cc_final: 0.6830 (mt0) REVERT: h 144 THR cc_start: 0.8589 (t) cc_final: 0.8223 (m) REVERT: i 84 ASP cc_start: 0.7031 (t0) cc_final: 0.6549 (t0) REVERT: j 31 GLN cc_start: 0.7750 (mt0) cc_final: 0.7152 (tm130) REVERT: g 164 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6924 (pt) REVERT: g 221 LEU cc_start: 0.6355 (tt) cc_final: 0.6120 (tp) outliers start: 137 outliers final: 78 residues processed: 700 average time/residue: 1.2621 time to fit residues: 1200.8677 Evaluate side-chains 653 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 560 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain S residue 263 GLN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 62 MET Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 31 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 260 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 758 optimal weight: 4.9990 chunk 467 optimal weight: 2.9990 chunk 861 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 468 optimal weight: 0.8980 chunk 781 optimal weight: 0.9990 chunk 643 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 768 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN F 31 GLN F 231 ASN F 263 GLN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN R 251 GLN ** S 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN X 263 GLN Z 151 ASN a 45 ASN ** a 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 ASN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115577 restraints weight = 110024.298| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.58 r_work: 0.3545 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 70056 Z= 0.160 Angle : 0.414 12.363 94824 Z= 0.236 Chirality : 0.032 0.215 12204 Planarity : 0.002 0.035 12132 Dihedral : 3.408 17.133 9792 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.65 % Allowed : 12.50 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.52 (0.08), residues: 9648 helix: 3.93 (0.06), residues: 6804 sheet: -1.40 (0.25), residues: 360 loop : 0.89 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.018 0.001 PHE E 177 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 585 time to evaluate : 6.136 Fit side-chains REVERT: A 31 GLN cc_start: 0.7963 (mt0) cc_final: 0.7761 (tm-30) REVERT: B 126 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7509 (mtmt) REVERT: B 240 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 252 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: C 67 ASP cc_start: 0.7922 (m-30) cc_final: 0.7692 (m-30) REVERT: C 191 ASP cc_start: 0.8733 (t0) cc_final: 0.8515 (t0) REVERT: D 16 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7285 (tp) REVERT: D 20 ASN cc_start: 0.8314 (m110) cc_final: 0.7933 (m110) REVERT: D 212 ASP cc_start: 0.8500 (t70) cc_final: 0.8236 (m-30) REVERT: E 31 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7241 (mt0) REVERT: E 84 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6460 (m-30) REVERT: E 88 ASP cc_start: 0.7946 (m-30) cc_final: 0.7601 (m-30) REVERT: F 31 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7614 (tp-100) REVERT: H 98 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6125 (tt) REVERT: J 45 ASN cc_start: 0.8795 (t0) cc_final: 0.8474 (t0) REVERT: J 77 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8111 (m-30) REVERT: K 195 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: K 243 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7701 (mmtt) REVERT: L 95 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6328 (tt0) REVERT: L 206 THR cc_start: 0.7844 (t) cc_final: 0.7446 (m) REVERT: M 38 LYS cc_start: 0.7492 (ptmt) cc_final: 0.7055 (pttm) REVERT: P 9 ASN cc_start: 0.7956 (t0) cc_final: 0.7638 (t0) REVERT: P 122 ASP cc_start: 0.7080 (p0) cc_final: 0.6711 (t0) REVERT: P 245 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6252 (mp10) REVERT: Q 31 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.4787 (mp10) REVERT: Q 176 THR cc_start: 0.7859 (t) cc_final: 0.7546 (m) REVERT: R 122 ASP cc_start: 0.7450 (m-30) cc_final: 0.7209 (m-30) REVERT: R 226 ASP cc_start: 0.8280 (m-30) cc_final: 0.8006 (m-30) REVERT: R 255 VAL cc_start: 0.8002 (p) cc_final: 0.7769 (t) REVERT: S 191 ASP cc_start: 0.7580 (m-30) cc_final: 0.7310 (m-30) REVERT: S 263 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: T 95 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: V 77 ASP cc_start: 0.7710 (m-30) cc_final: 0.7501 (m-30) REVERT: X 93 MET cc_start: 0.7715 (mtp) cc_final: 0.7219 (mtm) REVERT: Z 116 ASP cc_start: 0.7820 (m-30) cc_final: 0.7480 (m-30) REVERT: Z 256 GLN cc_start: 0.7623 (mm110) cc_final: 0.7253 (mt0) REVERT: Z 263 GLN cc_start: 0.7919 (mp10) cc_final: 0.7713 (mp10) REVERT: a 151 ASN cc_start: 0.8380 (t0) cc_final: 0.7955 (t0) REVERT: a 262 ASN cc_start: 0.7456 (t0) cc_final: 0.7246 (m-40) REVERT: b 32 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6414 (ttp-170) REVERT: b 105 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6664 (pp) REVERT: c 93 MET cc_start: 0.8220 (ttm) cc_final: 0.7997 (mtp) REVERT: c 195 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6805 (mm110) REVERT: d 31 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: d 245 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: d 256 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7775 (mt0) REVERT: e 105 LEU cc_start: 0.7906 (mt) cc_final: 0.7575 (mt) REVERT: f 263 GLN cc_start: 0.7375 (tp-100) cc_final: 0.6824 (mt0) REVERT: h 144 THR cc_start: 0.8583 (t) cc_final: 0.8218 (m) REVERT: i 84 ASP cc_start: 0.6994 (t0) cc_final: 0.6549 (t0) REVERT: j 31 GLN cc_start: 0.7743 (mt0) cc_final: 0.7162 (tm130) REVERT: g 221 LEU cc_start: 0.6406 (tt) cc_final: 0.6139 (tp) outliers start: 125 outliers final: 73 residues processed: 686 average time/residue: 1.2758 time to fit residues: 1192.7581 Evaluate side-chains 663 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 573 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain S residue 263 GLN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 31 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 260 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 795 optimal weight: 7.9990 chunk 430 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 465 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 488 optimal weight: 6.9990 chunk 758 optimal weight: 4.9990 chunk 541 optimal weight: 2.9990 chunk 354 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN F 31 GLN F 231 ASN F 263 GLN I 199 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN X 262 ASN X 263 GLN Z 151 ASN a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN d 106 ASN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 ASN i 231 ASN j 263 GLN ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110222 restraints weight = 110831.432| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.57 r_work: 0.3471 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 70056 Z= 0.266 Angle : 0.497 11.909 94824 Z= 0.277 Chirality : 0.035 0.217 12204 Planarity : 0.002 0.030 12132 Dihedral : 3.684 17.464 9792 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.59 % Allowed : 12.72 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.08), residues: 9648 helix: 3.39 (0.06), residues: 7020 sheet: -1.48 (0.25), residues: 360 loop : 0.34 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 49 HIS 0.005 0.002 HIS J 214 PHE 0.020 0.002 PHE R 110 ARG 0.007 0.001 ARG L 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 573 time to evaluate : 6.025 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8066 (mt0) cc_final: 0.7811 (tm-30) REVERT: B 126 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7661 (mtmt) REVERT: B 240 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7739 (mm-30) REVERT: C 67 ASP cc_start: 0.8038 (m-30) cc_final: 0.7766 (m-30) REVERT: C 191 ASP cc_start: 0.8833 (t0) cc_final: 0.8621 (t0) REVERT: D 20 ASN cc_start: 0.8395 (m110) cc_final: 0.7996 (m110) REVERT: D 212 ASP cc_start: 0.8541 (t70) cc_final: 0.8274 (m-30) REVERT: E 31 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7344 (mt0) REVERT: E 88 ASP cc_start: 0.7979 (m-30) cc_final: 0.7603 (m-30) REVERT: H 98 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6419 (tt) REVERT: J 45 ASN cc_start: 0.8875 (t0) cc_final: 0.8565 (t0) REVERT: K 243 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7783 (mmtt) REVERT: L 206 THR cc_start: 0.7830 (t) cc_final: 0.7481 (m) REVERT: M 38 LYS cc_start: 0.7585 (ptmt) cc_final: 0.7077 (pttm) REVERT: P 9 ASN cc_start: 0.7970 (t0) cc_final: 0.7696 (t0) REVERT: P 122 ASP cc_start: 0.7155 (p0) cc_final: 0.6722 (t0) REVERT: P 245 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6211 (mp10) REVERT: Q 31 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.4951 (mp10) REVERT: Q 176 THR cc_start: 0.8002 (t) cc_final: 0.7583 (m) REVERT: R 67 ASP cc_start: 0.7834 (m-30) cc_final: 0.7294 (t0) REVERT: R 122 ASP cc_start: 0.7638 (m-30) cc_final: 0.7424 (m-30) REVERT: R 192 THR cc_start: 0.8380 (p) cc_final: 0.8124 (p) REVERT: R 226 ASP cc_start: 0.8379 (m-30) cc_final: 0.8084 (m-30) REVERT: R 255 VAL cc_start: 0.8077 (p) cc_final: 0.7846 (t) REVERT: S 191 ASP cc_start: 0.7761 (m-30) cc_final: 0.7476 (m-30) REVERT: S 263 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: T 95 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: V 4 ASN cc_start: 0.7390 (t0) cc_final: 0.7115 (t0) REVERT: V 77 ASP cc_start: 0.7824 (m-30) cc_final: 0.7585 (m-30) REVERT: X 93 MET cc_start: 0.7874 (mtp) cc_final: 0.7412 (mtm) REVERT: X 95 GLU cc_start: 0.6956 (tt0) cc_final: 0.6590 (tt0) REVERT: Z 256 GLN cc_start: 0.7734 (mm110) cc_final: 0.7379 (mt0) REVERT: a 151 ASN cc_start: 0.8392 (t0) cc_final: 0.7909 (t0) REVERT: a 240 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6963 (mm-30) REVERT: b 32 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6411 (ttp-170) REVERT: b 105 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6865 (pp) REVERT: c 195 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6907 (mm110) REVERT: d 31 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: d 245 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7111 (mt0) REVERT: d 256 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7804 (mt0) REVERT: e 31 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6295 (mm110) REVERT: e 105 LEU cc_start: 0.7905 (mt) cc_final: 0.7596 (mt) REVERT: e 152 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7829 (m) REVERT: f 263 GLN cc_start: 0.7584 (tp-100) cc_final: 0.7112 (mt0) REVERT: h 71 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7555 (ttp-110) REVERT: h 144 THR cc_start: 0.8568 (t) cc_final: 0.8226 (m) REVERT: i 84 ASP cc_start: 0.7050 (t0) cc_final: 0.6624 (t0) REVERT: g 221 LEU cc_start: 0.6599 (tt) cc_final: 0.6340 (tp) outliers start: 120 outliers final: 65 residues processed: 671 average time/residue: 1.3483 time to fit residues: 1216.4580 Evaluate side-chains 622 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 544 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain S residue 263 GLN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 31 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 666 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 423 optimal weight: 2.9990 chunk 739 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 671 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 633 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN F 31 GLN F 263 GLN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN ** S 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Z 151 ASN ** Z 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 9 ASN ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110350 restraints weight = 110681.879| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.57 r_work: 0.3473 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 70056 Z= 0.248 Angle : 0.551 59.165 94824 Z= 0.320 Chirality : 0.035 0.882 12204 Planarity : 0.002 0.038 12132 Dihedral : 3.687 27.672 9792 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 0.82 % Favored : 99.16 % Rotamer: Outliers : 1.40 % Allowed : 12.99 % Favored : 85.61 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.08), residues: 9648 helix: 3.37 (0.06), residues: 7020 sheet: -1.49 (0.25), residues: 360 loop : 0.32 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 49 HIS 0.005 0.002 HIS h 214 PHE 0.019 0.002 PHE E 117 ARG 0.006 0.000 ARG L 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33465.77 seconds wall clock time: 577 minutes 7.79 seconds (34627.79 seconds total)